niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v__auto_tlrc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__AUTO_TLRC_METADATA = Metadata(
-    id="6358e72ba8c0b7fb15ce11a94e7f6e56fa8f3baa.boutiques",
+    id="9ec14a3c3a060032a8913afb5801da9608c8ae87.boutiques",
     name="@auto_tlrc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,49 @@ V__AUTO_TLRC_METADATA = Metadata(
 
 
 VAutoTlrcParameters = typing.TypedDict('VAutoTlrcParameters', {
-    "__STYXTYPE__": typing.Literal["@auto_tlrc"],
+    "@type": typing.NotRequired[typing.Literal["afni/@auto_tlrc"]],
+    "base_template": InputPathType,
+    "input_anat": InputPathType,
+    "no_ss": bool,
+    "warp_orig_vol": bool,
+    "dxyz": typing.NotRequired[float | None],
+    "dx": typing.NotRequired[float | None],
+    "dy": typing.NotRequired[float | None],
+    "dz": typing.NotRequired[float | None],
+    "pad_base": typing.NotRequired[float | None],
+    "keep_tmp": bool,
+    "clean": bool,
+    "xform": typing.NotRequired[str | None],
+    "no_avoid_eyes": bool,
+    "ncr": bool,
+    "onepass": bool,
+    "twopass": bool,
+    "maxite": typing.NotRequired[float | None],
+    "not_OK_maxite": bool,
+    "inweight": bool,
+    "rigid_equiv": bool,
+    "init_xform": typing.NotRequired[str | None],
+    "no_pre": bool,
+    "out_space": typing.NotRequired[str | None],
+    "3dAllineate": bool,
+    "3dAlcost": typing.NotRequired[str | None],
+    "overwrite": bool,
+    "apar": InputPathType,
+    "input_dataset": InputPathType,
+    "pad_input": typing.NotRequired[float | None],
+    "onewarp": bool,
+    "twowarp": bool,
+    "rmode": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "suffix": typing.NotRequired[str | None],
+    "keep_view": bool,
+    "base_copy": typing.NotRequired[str | None],
+    "base_list": bool,
+    "use_gz": bool,
+    "verb": bool,
+})
+VAutoTlrcParametersTagged = typing.TypedDict('VAutoTlrcParametersTagged', {
+    "@type": typing.Literal["afni/@auto_tlrc"],
     "base_template": InputPathType,
     "input_anat": InputPathType,
     "no_ss": bool,
@@ -55,43 +97,11 @@ VAutoTlrcParameters = typing.TypedDict('VAutoTlrcParameters', {
     "use_gz": bool,
     "verb": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@auto_tlrc": v__auto_tlrc_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-        "@auto_tlrc": v__auto_tlrc_outputs,
-    }.get(t)
 
 
 class VAutoTlrcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__auto_tlrc(...)`.
+    Output object returned when calling `VAutoTlrcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -141,7 +151,7 @@ def v__auto_tlrc_params(
     base_list: bool = False,
     use_gz: bool = False,
     verb: bool = False,
-) -> VAutoTlrcParameters:
+) -> VAutoTlrcParametersTagged:
     """
     Build parameters.
     
@@ -213,7 +223,7 @@ def v__auto_tlrc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@auto_tlrc",
+        "@type": "afni/@auto_tlrc",
         "base_template": base_template,
         "input_anat": input_anat,
         "no_ss": no_ss,
@@ -289,134 +299,134 @@ def v__auto_tlrc_cargs(
     cargs.append("@auto_tlrc")
     cargs.extend([
         "-base",
-        execution.input_file(params.get("base_template"))
+        execution.input_file(params.get("base_template", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_anat"))
+        execution.input_file(params.get("input_anat", None))
     ])
-    if params.get("no_ss"):
+    if params.get("no_ss", False):
         cargs.append("-no_ss")
-    if params.get("warp_orig_vol"):
+    if params.get("warp_orig_vol", False):
         cargs.append("-warp_orig_vol")
-    if params.get("dxyz") is not None:
+    if params.get("dxyz", None) is not None:
         cargs.extend([
             "-dxyz",
-            str(params.get("dxyz"))
+            str(params.get("dxyz", None))
         ])
-    if params.get("dx") is not None:
+    if params.get("dx", None) is not None:
         cargs.extend([
             "-dx",
-            str(params.get("dx"))
+            str(params.get("dx", None))
         ])
-    if params.get("dy") is not None:
+    if params.get("dy", None) is not None:
         cargs.extend([
             "-dy",
-            str(params.get("dy"))
+            str(params.get("dy", None))
         ])
-    if params.get("dz") is not None:
+    if params.get("dz", None) is not None:
         cargs.extend([
             "-dz",
-            str(params.get("dz"))
+            str(params.get("dz", None))
         ])
-    if params.get("pad_base") is not None:
+    if params.get("pad_base", None) is not None:
         cargs.extend([
             "-pad_base",
-            str(params.get("pad_base"))
+            str(params.get("pad_base", None))
         ])
-    if params.get("keep_tmp"):
+    if params.get("keep_tmp", False):
         cargs.append("-keep_tmp")
-    if params.get("clean"):
+    if params.get("clean", False):
         cargs.append("-clean")
-    if params.get("xform") is not None:
+    if params.get("xform", None) is not None:
         cargs.extend([
             "-xform",
-            params.get("xform")
+            params.get("xform", None)
         ])
-    if params.get("no_avoid_eyes"):
+    if params.get("no_avoid_eyes", False):
         cargs.append("-no_avoid_eyes")
-    if params.get("ncr"):
+    if params.get("ncr", False):
         cargs.append("-ncr")
-    if params.get("onepass"):
+    if params.get("onepass", False):
         cargs.append("-onepass")
-    if params.get("twopass"):
+    if params.get("twopass", False):
         cargs.append("-twopass")
-    if params.get("maxite") is not None:
+    if params.get("maxite", None) is not None:
         cargs.extend([
             "-maxite",
-            str(params.get("maxite"))
+            str(params.get("maxite", None))
         ])
-    if params.get("not_OK_maxite"):
+    if params.get("not_OK_maxite", False):
         cargs.append("-not_OK_maxite")
-    if params.get("inweight"):
+    if params.get("inweight", False):
         cargs.append("-inweight")
-    if params.get("rigid_equiv"):
+    if params.get("rigid_equiv", False):
         cargs.append("-rigid_equiv")
-    if params.get("init_xform") is not None:
+    if params.get("init_xform", None) is not None:
         cargs.extend([
             "-init_xform",
-            params.get("init_xform")
+            params.get("init_xform", None)
         ])
-    if params.get("no_pre"):
+    if params.get("no_pre", False):
         cargs.append("-no_pre")
-    if params.get("out_space") is not None:
+    if params.get("out_space", None) is not None:
         cargs.extend([
             "-out_space",
-            params.get("out_space")
+            params.get("out_space", None)
         ])
-    if params.get("3dAllineate"):
+    if params.get("3dAllineate", False):
         cargs.append("-3dAllineate")
-    if params.get("3dAlcost") is not None:
+    if params.get("3dAlcost", None) is not None:
         cargs.extend([
             "-3dAlcost",
-            params.get("3dAlcost")
+            params.get("3dAlcost", None)
         ])
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
     cargs.extend([
         "-apar",
-        execution.input_file(params.get("apar"))
+        execution.input_file(params.get("apar", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
-    if params.get("pad_input") is not None:
+    if params.get("pad_input", None) is not None:
         cargs.extend([
             "-pad_input",
-            str(params.get("pad_input"))
+            str(params.get("pad_input", None))
         ])
-    if params.get("onewarp"):
+    if params.get("onewarp", False):
         cargs.append("-onewarp")
-    if params.get("twowarp"):
+    if params.get("twowarp", False):
         cargs.append("-twowarp")
-    if params.get("rmode") is not None:
+    if params.get("rmode", None) is not None:
         cargs.extend([
             "-rmode",
-            params.get("rmode")
+            params.get("rmode", None)
         ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("suffix") is not None:
+    if params.get("suffix", None) is not None:
         cargs.extend([
             "-suffix",
-            params.get("suffix")
+            params.get("suffix", None)
         ])
-    if params.get("keep_view"):
+    if params.get("keep_view", False):
         cargs.append("-keep_view")
-    if params.get("base_copy") is not None:
+    if params.get("base_copy", None) is not None:
         cargs.extend([
             "-base_copy",
-            params.get("base_copy")
+            params.get("base_copy", None)
         ])
-    if params.get("base_list"):
+    if params.get("base_list", False):
         cargs.append("-base_list")
-    if params.get("use_gz"):
+    if params.get("use_gz", False):
         cargs.append("-use_gz")
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
     return cargs
 
@@ -436,20 +446,22 @@ def v__auto_tlrc_outputs(
     """
     ret = VAutoTlrcOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        transform_file=execution.output_file(params.get("prefix") + ".Xat.1D") if (params.get("prefix") is not None) else None,
+        output_dataset=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        transform_file=execution.output_file(params.get("prefix", None) + ".Xat.1D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v__auto_tlrc_execute(
     params: VAutoTlrcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAutoTlrcOutputs:
     """
-    A script to transform an anatomical dataset to align with some standard space
-    template and to apply the same TLRC transform obtained with @auto_tlrc in Usage
-    1 mode to other datasets.
+    @auto_tlrc
+    
+    A script to transform an anatomical dataset to align with some standard
+    space template and to apply the same TLRC transform obtained with @auto_tlrc
+    in Usage 1 mode to other datasets.
     
     Author: AFNI Developers
     
@@ -457,10 +469,12 @@ def v__auto_tlrc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAutoTlrcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__AUTO_TLRC_METADATA)
     params = execution.params(params)
     cargs = v__auto_tlrc_cargs(params, execution)
     ret = v__auto_tlrc_outputs(params, execution)
@@ -511,9 +525,11 @@ def v__auto_tlrc(
     runner: Runner | None = None,
 ) -> VAutoTlrcOutputs:
     """
-    A script to transform an anatomical dataset to align with some standard space
-    template and to apply the same TLRC transform obtained with @auto_tlrc in Usage
-    1 mode to other datasets.
+    @auto_tlrc
+    
+    A script to transform an anatomical dataset to align with some standard
+    space template and to apply the same TLRC transform obtained with @auto_tlrc
+    in Usage 1 mode to other datasets.
     
     Author: AFNI Developers
     
@@ -587,8 +603,6 @@ def v__auto_tlrc(
     Returns:
         NamedTuple of outputs (described in `VAutoTlrcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__AUTO_TLRC_METADATA)
     params = v__auto_tlrc_params(
         base_template=base_template,
         input_anat=input_anat,
@@ -630,13 +644,13 @@ def v__auto_tlrc(
         use_gz=use_gz,
         verb=verb,
     )
-    return v__auto_tlrc_execute(params, execution)
+    return v__auto_tlrc_execute(params, runner)
 
 
 __all__ = [
     "VAutoTlrcOutputs",
-    "VAutoTlrcParameters",
     "V__AUTO_TLRC_METADATA",
     "v__auto_tlrc",
+    "v__auto_tlrc_execute",
     "v__auto_tlrc_params",
 ]

niwrap_afni/afni/v__build_afni_xlib.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__BUILD_AFNI_XLIB_METADATA = Metadata(
-    id="ada8e2943681d0a1a8fa93d2a93d83cd8c338502.boutiques",
+    id="6d2e574b4e7a94571cef3ddf151a833feef4d14a.boutiques",
     name="@build_afni_Xlib",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__BUILD_AFNI_XLIB_METADATA = Metadata(
 
 
 VBuildAfniXlibParameters = typing.TypedDict('VBuildAfniXlibParameters', {
-    "__STYXTYPE__": typing.Literal["@build_afni_Xlib"],
+    "@type": typing.NotRequired[typing.Literal["afni/@build_afni_Xlib"]],
+    "afniX": bool,
+    "localinstall": bool,
+    "debug_symbols": bool,
+    "lib32": bool,
+    "lib64": bool,
+    "packages": list[str],
+})
+VBuildAfniXlibParametersTagged = typing.TypedDict('VBuildAfniXlibParametersTagged', {
+    "@type": typing.Literal["afni/@build_afni_Xlib"],
     "afniX": bool,
     "localinstall": bool,
     "debug_symbols": bool,
@@ -22,42 +31,11 @@ VBuildAfniXlibParameters = typing.TypedDict('VBuildAfniXlibParameters', {
     "lib64": bool,
     "packages": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@build_afni_Xlib": v__build_afni_xlib_cargs,
-    }.get(t)
-
-
-def dyn_outputs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build outputs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build outputs function.
-    """
-    return {
-    }.get(t)
 
 
 class VBuildAfniXlibOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__build_afni_xlib(...)`.
+    Output object returned when calling `VBuildAfniXlibParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def v__build_afni_xlib_params(
     debug_symbols: bool = False,
     lib32: bool = False,
     lib64: bool = False,
-) -> VBuildAfniXlibParameters:
+) -> VBuildAfniXlibParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +65,7 @@ def v__build_afni_xlib_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@build_afni_Xlib",
+        "@type": "afni/@build_afni_Xlib",
         "afniX": afni_x,
         "localinstall": localinstall,
         "debug_symbols": debug_symbols,
@@ -113,17 +91,17 @@ def v__build_afni_xlib_cargs(
     """
     cargs = []
     cargs.append("@build_afni_Xlib")
-    if params.get("afniX"):
+    if params.get("afniX", False):
         cargs.append("-afniX")
-    if params.get("localinstall"):
+    if params.get("localinstall", False):
         cargs.append("-localinstall")
-    if params.get("debug_symbols"):
+    if params.get("debug_symbols", False):
         cargs.append("-g")
-    if params.get("lib32"):
+    if params.get("lib32", False):
         cargs.append("-lib32")
-    if params.get("lib64"):
+    if params.get("lib64", False):
         cargs.append("-lib64")
-    cargs.extend(params.get("packages"))
+    cargs.extend(params.get("packages", None))
     return cargs
 
 
@@ -148,9 +126,11 @@ def v__build_afni_xlib_outputs(
 
 def v__build_afni_xlib_execute(
     params: VBuildAfniXlibParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VBuildAfniXlibOutputs:
     """
+    @build_afni_Xlib
+    
     Compile and install lesstif, openmotif, and/or libXt.
     
     Author: AFNI Developers
@@ -159,10 +139,12 @@ def v__build_afni_xlib_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VBuildAfniXlibOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__BUILD_AFNI_XLIB_METADATA)
     params = execution.params(params)
     cargs = v__build_afni_xlib_cargs(params, execution)
     ret = v__build_afni_xlib_outputs(params, execution)
@@ -180,6 +162,8 @@ def v__build_afni_xlib(
     runner: Runner | None = None,
 ) -> VBuildAfniXlibOutputs:
     """
+    @build_afni_Xlib
+    
     Compile and install lesstif, openmotif, and/or libXt.
     
     Author: AFNI Developers
@@ -199,8 +183,6 @@ def v__build_afni_xlib(
     Returns:
         NamedTuple of outputs (described in `VBuildAfniXlibOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__BUILD_AFNI_XLIB_METADATA)
     params = v__build_afni_xlib_params(
         afni_x=afni_x,
         localinstall=localinstall,
@@ -209,13 +191,13 @@ def v__build_afni_xlib(
         lib64=lib64,
         packages=packages,
     )
-    return v__build_afni_xlib_execute(params, execution)
+    return v__build_afni_xlib_execute(params, runner)
 
 
 __all__ = [
     "VBuildAfniXlibOutputs",
-    "VBuildAfniXlibParameters",
     "V__BUILD_AFNI_XLIB_METADATA",
     "v__build_afni_xlib",
+    "v__build_afni_xlib_execute",
     "v__build_afni_xlib_params",
 ]